57 Open source projects that are alternatives of or similar to dcHiC

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Das Robert Koch-Institut stellt Systeme zur bundesweiten molekularen Surveillance des SRARS-CoV-2-Virus bereit. Jedes Labor in Deutschland, das SARS-CoV-2 sequenziert, ist laut der Verordnung zur molekulargenetischen Surveillance des Coronavirus SARS-CoV-2 verpflichtet, dem Robert Koch-Institut die Sequenz- und zugehörige Metadaten zu übermittel…

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Nanopore sequence read simulator

CUT&RUN and CUT&Tag data processing and analysis

Docker for 4DN Hi-C processing pipeline

A fast 23andMe DNA parser and inferrer for Python

Genome Interval Arithmetic in R

Large genome reassembly based on Hi-C data, continuation of GRAAL

Understand DNA structure and how machine learning can be used to work with DNA sequence data.

De novo annotation of young retrotransposons

A 3D genome data processing tutorial for ISMB/ECCB 2017

Analysis of Chromosome Conformation Capture data (Hi-C)

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

🔬 Assemble large genomes using short reads

Download and use genomes the easy way.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

Viral genomics analysis pipelines

Next generation sequencing reads de novo assembler.

Genomic Data Retrieval with R

Genome annotation with AUGUSTUS

🌈Scaffold genome sequence assemblies using linked read sequencing data

Official code repository for GATK versions 4 and up

Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

parallelized blat with multi-threads support

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

A package for designing compact and comprehensive capture probe sets.

PERF is an Exhaustive Repeat Finder

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Graph based multi genome aligner

An efficient index for the colored, compacted, de Bruijn graph

Workflow for Building Microsynteny Networks

SuperPhy for the semantic web

Research on polio / protein folding.

Server component for HiGlass that manages and serves tiled data

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Builds a docker container wrapping higlass-server and higlass-client in nginx

Adjacency-constrained hierarchical clustering of a similarity matrix

Genome Contact Map Explorer - gcMapExplorer. Visit:

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)